Lock properties from applying object transformations
Cannot be done with lattices.

Also somehow locking the scale to its value and performing scale applying would cause the lattice itself to expand/shrink again (resulting in 2x the original transformation).

Use Mesh Deform instead and keep the scale of that cage at 1. Only this setup will be fool-proof. But Mesh-Deform is not a full supplement for Lattice, depends on what you are doing with it..